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Mol Biol Evol. 2005 Dec;22(12):2457-71. Epub 2005 Aug 17.

Statistical alignment of retropseudogenes and their functional paralogs.

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  • 1Department of Computer Science and Operations Research, Université de Montréal, succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada. csuros@iro.umontreal.ca


We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions, and deletions and combines nucleotide- and codon-level mutation models. We give a dynamic programming method for calculating the likelihood of homology between two sequences in the model and describe the accompanying alignment algorithm. We also describe how ancestral codons can be computed when the same gene produced multiple pseudogene homologs. We apply our methods to the evolution of human cytochrome c.

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